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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
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- Ames mutagenicity
Toxtree provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java), with the use of The Chemistry Development Kit.
BANNER is a named entity recognition system intended primarily for biomedical text. It uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.
An api for domain level interaction with SNOMED CT and an implementation based on a storage engine using a native SNOMED distribution stored in neo4j as a backend.
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Trial Criteria Online Data Entry (trialCODE): a Java-based user interface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
GRIP is a clinical decision support system for controlling glucose levels in critically ill patients. GRIP may replace paper-based protocols for intensive insulin therapy and can use arbitrary complex rules to advise nurses on insulin doses.
Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.
The program siRNArules 1.0 can predict active short interfering RNA (siRNA) with a rather high efficiency (see published paper on this in RNA journal). This project aims to develop new versions, siRNArules 2.0 etc.
Simulare is a simulation engine and application built on java. At first it'll simulate an aquarium but planned to evolve latter. One objective is a simple UI so everybody can use it. Imagine a fish farmer optimizing his production with this software! ;)
This projects intends to develop a complete distributed peer-to-peer environment
for running heuristic optimization, modelling, artificial life, etc applications. This involves a network engine, libraries and different user interfaces. All this in java.
Info Sapient will be an Open Source, Common License 0.5, 100% Pure Java based program that is a mechanism for the expression and execution of business rules.
Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cells